Remove dcc common and dcc id dependency#503 #574

KevinFHartmann · 2020-01-07T00:42:23Z

Now compiles, builds, and passes make test-*.

rtisma

As you can see, i am allergic to string literals. If the same literal gets repeated more than once, it should instead be referenced as a variable. I left a few comments for the Splitters and Joiners class that needs to be made, but there are several other lines that need similar fixing and i didnt comment on them so that this review isnt riddled with identical comments.

rtisma · 2020-01-07T15:42:32Z

song-server/pom.xml

+       <dependency>
+           <groupId>org.glassfish.jaxb</groupId>
+           <artifactId>jaxb-runtime</artifactId>
+           <version>2.3.1</version>


move this version definition into the <dependencyManagement> block of the root pom.xml. If this dependency is only used in song-server, then rip out the dependency from the dependencyManagement section and put it here. Also, use the version variable like ${jaxb.version}

String constants are a valid part of the Java language. Don't be so afraid of them!

If we expect the definition of a constant to ever change, then YES, by all means, we should use a name rather than an inline value.

OBJECT_NAME_DELIMITER might change. NEWLINE might change (based upon different operating systems idea of what a new line should be).

But the definition of a something like COMMA should never change, and if it does, it's confusing.

All we accomplish by separating the definition of the constant from the code in this case is forcing the developer to do extra work to double check that COMMA is defined as ",".

i find that string constants are harder to read and make it hard to search for via the IDE. by using COMMA, you can inspect its usage easily. Regarding double checking, for something that sensitive, there should be tests in place that ensure it functions as expected.

I'm confused. How is searching for "," any harder than searching for COMMA? If anything, it should be easier, since it's two less characters to type. :-)

There should always be tests. That doesn't mean that the code does what you think it does when you read it.:-)

But for consistency, I'll make you happy. :-)

rtisma · 2020-01-07T15:48:30Z

song-server/src/main/java/bio/overture/song/server/controller/AnalysisController.java

@@ -82,7 +81,7 @@
      @ApiParam(value = "Non-empty comma separated list of analysis states to filter by")
          @RequestParam(value = "analysisStates", defaultValue = "PUBLISHED", required = false)
          String analysisStates) {
-    return analysisService.getAnalysis(studyId, ImmutableSet.copyOf(COMMA.split(analysisStates)));
+    return analysisService.getAnalysis(studyId, ImmutableSet.copyOf(",".split(analysisStates)));


Create a Splitters class with a no args constructor, that contains:
public static final Splitter COMMA = Splitter.on(",");
and likewise for any other splits.

rtisma · 2020-01-07T15:49:39Z

...main/java/bio/overture/song/server/controller/analysisType/AnalysisTypePageableResolver.java

@@ -59,7 +58,7 @@
  public static final String DEFAULT_SORT_VARIABLE = VERSION;
  public static final Direction DEFAULT_SORT_ORDER = DESC;

-  private static final String ALLOWED_SORT_VARIABLES = COMMA.join(VERSION, NAME);
+  private static final String ALLOWED_SORT_VARIABLES = VERSION + "," + NAME;


Create a no args constuctor Joiners class that contains the following:
public static final Joiner COMMA = Joiner.on(",");
likewise for any other characters to join on

rtisma · 2020-01-07T15:50:14Z

song-server/src/main/java/bio/overture/song/server/exceptions/ServerExceptionHandler.java

@@ -172,7 +171,7 @@ private static String errorResponseBody(
  }

  private static List<String> getFullStackTraceList(Throwable t) {
-    return NEWLINE.splitToList(getStackTraceAsString(t)).stream()
+    return stream(getStackTraceAsString(t).split("\n"))


newline splitter

rtisma · 2020-01-07T15:50:50Z

song-server/src/main/java/bio/overture/song/server/service/AnalysisService.java

@@ -415,7 +415,7 @@ private void checkMissingFiles(String analysisId, List<FileEntity> files) {
        "The following storage objectIds must be uploaded to the storage server before the "
            + "analysisId %s can be published: %s",
        analysisId,
-        COMMA.join(missingFileIds));
+        join(",", missingFileIds));


use Joiners.COMMA

rtisma

also, there are conflicts with the branch

… for commonly used string constants. Change: Now use the Separators enum and avoid the use of String constants.

rtisma · 2020-01-08T14:06:18Z

song-core/src/main/java/bio/overture/song/core/utils/Separators.java

+import java.util.List;
+
+/** Joiners and Splitters for commonly used separators. */
+public enum Separators {


KevinFHartmann added 3 commits January 6, 2020 16:16

Enhancement: No longer includes dcc-common/dcc-id modules. Compiles.

0312dae

Bugfix: Now compiles and runs unit tests (mvn clean package runs)

5923936

Bugfix: Now runs all unit-test and make test-* steps correctly

2ae28f4

KevinFHartmann requested a review from rtisma January 7, 2020 00:42

rtisma suggested changes Jan 7, 2020

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rtisma reviewed Jan 7, 2020

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KevinFHartmann added 2 commits January 7, 2020 16:19

Merge branch 'develop' into Remove_dcc-common_and_dcc-id_dependency#503

dd5fab6

Change: Now use a Separators enum consisting of Joiners and Splitters…

d42e264

… for commonly used string constants. Change: Now use the Separators enum and avoid the use of String constants.

rtisma approved these changes Jan 8, 2020

View reviewed changes

KevinFHartmann merged commit a7c4e57 into develop Jan 8, 2020

KevinFHartmann deleted the Remove_dcc-common_and_dcc-id_dependency#503 branch January 8, 2020 15:36

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Remove dcc common and dcc id dependency#503 #574

Remove dcc common and dcc id dependency#503 #574

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Remove dcc common and dcc id dependency#503 #574

Remove dcc common and dcc id dependency#503 #574

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